Mechanistic insight into the biological nanopore in tetragonal lysozyme crystal

We characterize the major biological nanopore in tetragonal lysozyme crystal at the atomic resolution and investigate the mechanistic behavior of H2O and Cl− ions in the pore. The pore is approximately cylindrical with a radius in the range of 0.6–0.7 nm. H2O density along the pore axis is governed by the surface characteristics, while the electrostatic interactions with charged Lys and Asp residues largely determine the axial density of Cl−. In the vicinity of pore surface, Cl− and H2O exhibit ordered structures, particularly, there are one and two peaks separately in the radial density profiles of Cl− and H2O. Exchanges of H2O and Cl− between inside and outside the pore are found, and the average residence times in the pore are 28.2 and 58.1 ps for H2O and Cl−, respectively. Quasi-one-dimensional diffusion of H2O and Cl− is observed preferentially along the pore axis, and the diffusivity is smaller than in bulk phase. In 0.1 nm thick layer in the pore, H2O can stay continuously up to 15 ps. Due to the restrained motion near the pore surface, H2O shows an anomalous subdiffusion and the anomaly reduces upon moving away from the surface.